The overall goal of this project is to identify genes that, when aberrant, contribute to progression and/or to development of drug resistance in breast cancer. The studies proposed now are built on our earlier observations of numerous DNA sequence copy number abnormalities in human breast cancer using fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). Many of the frequent abnormalities that we have identified are not associated with known oncogenes. Thus, we now seek to identify and characterize genes in these regions of common abnormality and to use this information to improve prognostication and therapy. (1) We have localized a region of commonly increased copy number to an approximately 2 Mb wide portion of chromosome 20q13. We will now further narrow this region by high resolution analysis of additional tumors, complete development of a P1/YAC contig spanning this region, identify and characterize genes that map to this region and identify the gene(s) that contribute to breast cancer progression. (2) We will use CGH and FISH to identify DNA sequence copy number abnormalities that are associated with the development of chemoresistance in breast cancers and to determine the extent to which molecular cytogenetic disarray observed in a subset of human breast cancers is caused by defects in cell cycle checkpoint genes. (3) We have identified the cell adhesion molecular, E-cadherin, as a candidate tumor suppressor gene that is inactivated in breast cancer cell lines by deletion of 16q22 plus mutation of the remaining allele. We will now determine if E-cadherin is inactivated in the same way in primary breast tumors and explore the possibility that mutations in collaborating genes alpha, beta and gamma- catenin and vinculin also contribute to loss of E-cadherin mediated adhesion.